Starting phenix.real_space_refine on Tue Feb 11 02:41:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7msx_23971/02_2025/7msx_23971.cif Found real_map, /net/cci-nas-00/data/ceres_data/7msx_23971/02_2025/7msx_23971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7msx_23971/02_2025/7msx_23971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7msx_23971/02_2025/7msx_23971.map" model { file = "/net/cci-nas-00/data/ceres_data/7msx_23971/02_2025/7msx_23971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7msx_23971/02_2025/7msx_23971.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 26 5.16 5 C 2359 2.51 5 N 620 2.21 5 O 698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3706 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3703 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 13, 'TRANS': 459} Chain breaks: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1016 SG CYS A 143 13.882 35.673 58.737 1.00 38.05 S ATOM 1040 SG CYS A 146 12.818 36.968 62.628 1.00 47.40 S ATOM 1153 SG CYS A 161 16.687 37.445 59.660 1.00 42.84 S ATOM 1179 SG CYS A 164 15.449 34.581 62.038 1.00 44.32 S ATOM 1371 SG CYS A 190 28.609 18.258 44.496 1.00 54.40 S ATOM 1389 SG CYS A 193 30.905 15.408 45.275 1.00 70.39 S ATOM 1713 SG CYS A 236 31.982 19.316 43.189 1.00 52.65 S ATOM 136 SG CYS A 20 17.151 42.649 18.557 1.00 45.24 S ATOM 372 SG CYS A 51 16.203 45.352 15.948 1.00 45.63 S Time building chain proxies: 3.22, per 1000 atoms: 0.87 Number of scatterers: 3706 At special positions: 0 Unit cell: (57.546, 75.894, 114.258, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 26 16.00 O 698 8.00 N 620 7.00 C 2359 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 632.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 143 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 146 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 161 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 164 " pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 202 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 236 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 190 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 193 " pdb=" ZN A 703 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 56 " pdb="ZN ZN A 703 " - pdb=" ND1 HIS A 54 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 51 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 20 " Number of angles added : 10 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 878 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 4 sheets defined 46.1% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 18 through 28 Processing helix chain 'A' and resid 34 through 45 Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 203 through 212 removed outlier: 4.250A pdb=" N GLY A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 275 removed outlier: 3.562A pdb=" N LEU A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 299 Processing helix chain 'A' and resid 303 through 312 removed outlier: 3.732A pdb=" N LYS A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 325 Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 378 through 394 Processing helix chain 'A' and resid 396 through 407 Processing helix chain 'A' and resid 414 through 423 Processing helix chain 'A' and resid 424 through 438 Processing helix chain 'A' and resid 441 through 443 No H-bonds generated for 'chain 'A' and resid 441 through 443' Processing helix chain 'A' and resid 444 through 456 removed outlier: 3.671A pdb=" N LEU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A 456 " --> pdb=" O GLU A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 460 Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'A' and resid 492 through 503 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 removed outlier: 7.456A pdb=" N VAL A 6 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR A 61 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYS A 78 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ALA A 184 " --> pdb=" O PRO A 245 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASN A 133 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS A 187 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 6 through 7 removed outlier: 7.456A pdb=" N VAL A 6 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR A 61 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYS A 78 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 235 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL A 244 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR A 233 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ARG A 246 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N PHE A 231 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER A 248 " --> pdb=" O CYS A 229 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N CYS A 229 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR A 233 " --> pdb=" O ARG A 222 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ARG A 222 " --> pdb=" O TYR A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 169 removed outlier: 3.678A pdb=" N LEU A 137 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 334 removed outlier: 6.106A pdb=" N VAL A 279 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR A 332 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE A 281 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLY A 334 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE A 283 " --> pdb=" O GLY A 334 " (cutoff:3.500A) 181 hydrogen bonds defined for protein. 492 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.02 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 722 1.33 - 1.45: 924 1.45 - 1.57: 2100 1.57 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 3777 Sorted by residual: bond pdb=" N PRO A 91 " pdb=" CD PRO A 91 " ideal model delta sigma weight residual 1.473 1.400 0.073 1.40e-02 5.10e+03 2.74e+01 bond pdb=" N PRO A 200 " pdb=" CD PRO A 200 " ideal model delta sigma weight residual 1.473 1.414 0.059 1.40e-02 5.10e+03 1.78e+01 bond pdb=" N PRO A 13 " pdb=" CD PRO A 13 " ideal model delta sigma weight residual 1.473 1.414 0.059 1.40e-02 5.10e+03 1.76e+01 bond pdb=" N PRO A 17 " pdb=" CD PRO A 17 " ideal model delta sigma weight residual 1.473 1.416 0.057 1.40e-02 5.10e+03 1.69e+01 bond pdb=" N PRO A 74 " pdb=" CD PRO A 74 " ideal model delta sigma weight residual 1.473 1.417 0.056 1.40e-02 5.10e+03 1.58e+01 ... (remaining 3772 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 4853 1.27 - 2.53: 203 2.53 - 3.80: 43 3.80 - 5.06: 1 5.06 - 6.33: 3 Bond angle restraints: 5103 Sorted by residual: angle pdb=" N GLY A 327 " pdb=" CA GLY A 327 " pdb=" C GLY A 327 " ideal model delta sigma weight residual 115.21 121.46 -6.25 1.30e+00 5.92e-01 2.31e+01 angle pdb=" C ALA A 26 " pdb=" N ARG A 27 " pdb=" CA ARG A 27 " ideal model delta sigma weight residual 120.28 116.58 3.70 1.34e+00 5.57e-01 7.63e+00 angle pdb=" CA TRP A 432 " pdb=" CB TRP A 432 " pdb=" CG TRP A 432 " ideal model delta sigma weight residual 113.60 118.78 -5.18 1.90e+00 2.77e-01 7.44e+00 angle pdb=" C VAL A 234 " pdb=" CA VAL A 234 " pdb=" CB VAL A 234 " ideal model delta sigma weight residual 111.44 109.09 2.35 9.50e-01 1.11e+00 6.11e+00 angle pdb=" C VAL A 157 " pdb=" CA VAL A 157 " pdb=" CB VAL A 157 " ideal model delta sigma weight residual 111.44 109.29 2.15 9.50e-01 1.11e+00 5.14e+00 ... (remaining 5098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.59: 2119 14.59 - 29.17: 99 29.17 - 43.76: 21 43.76 - 58.34: 7 58.34 - 72.92: 3 Dihedral angle restraints: 2249 sinusoidal: 885 harmonic: 1364 Sorted by residual: dihedral pdb=" CA GLY A 344 " pdb=" C GLY A 344 " pdb=" N GLU A 345 " pdb=" CA GLU A 345 " ideal model delta harmonic sigma weight residual 180.00 163.30 16.70 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA SER A 351 " pdb=" C SER A 351 " pdb=" N PRO A 352 " pdb=" CA PRO A 352 " ideal model delta harmonic sigma weight residual 180.00 165.40 14.60 0 5.00e+00 4.00e-02 8.53e+00 dihedral pdb=" CA PHE A 329 " pdb=" C PHE A 329 " pdb=" N LYS A 330 " pdb=" CA LYS A 330 " ideal model delta harmonic sigma weight residual 180.00 165.44 14.56 0 5.00e+00 4.00e-02 8.48e+00 ... (remaining 2246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 375 0.033 - 0.067: 91 0.067 - 0.100: 56 0.100 - 0.134: 36 0.134 - 0.167: 15 Chirality restraints: 573 Sorted by residual: chirality pdb=" CA VAL A 186 " pdb=" N VAL A 186 " pdb=" C VAL A 186 " pdb=" CB VAL A 186 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CA VAL A 230 " pdb=" N VAL A 230 " pdb=" C VAL A 230 " pdb=" CB VAL A 230 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CA VAL A 6 " pdb=" N VAL A 6 " pdb=" C VAL A 6 " pdb=" CB VAL A 6 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.35e-01 ... (remaining 570 not shown) Planarity restraints: 649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 432 " -0.016 2.00e-02 2.50e+03 1.30e-02 4.20e+00 pdb=" CG TRP A 432 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 432 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 432 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 432 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 432 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 432 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 432 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 432 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 432 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 464 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.35e+00 pdb=" C ASP A 464 " 0.032 2.00e-02 2.50e+03 pdb=" O ASP A 464 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 465 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 463 " -0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" C ARG A 463 " 0.024 2.00e-02 2.50e+03 pdb=" O ARG A 463 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP A 464 " -0.008 2.00e-02 2.50e+03 ... (remaining 646 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1457 2.89 - 3.39: 3529 3.39 - 3.89: 6079 3.89 - 4.40: 7034 4.40 - 4.90: 11643 Nonbonded interactions: 29742 Sorted by model distance: nonbonded pdb=" O GLU A 272 " pdb=" NZ LYS A 276 " model vdw 2.385 3.120 nonbonded pdb=" NZ LYS A 288 " pdb=" OD2 ASP A 409 " model vdw 2.388 3.120 nonbonded pdb=" OD2 ASP A 23 " pdb=" NH1 ARG A 27 " model vdw 2.476 3.120 nonbonded pdb=" NZ LYS A 320 " pdb=" OE2 GLU A 324 " model vdw 2.561 3.120 nonbonded pdb=" N GLU A 373 " pdb=" OE1 GLU A 373 " model vdw 2.566 3.120 ... (remaining 29737 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.800 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 3777 Z= 0.519 Angle : 0.622 6.330 5103 Z= 0.397 Chirality : 0.052 0.167 573 Planarity : 0.003 0.023 649 Dihedral : 10.301 72.925 1371 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.36), residues: 467 helix: 0.34 (0.34), residues: 180 sheet: -0.85 (0.52), residues: 74 loop : 0.34 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 432 HIS 0.001 0.000 HIS A 56 PHE 0.010 0.001 PHE A 93 TYR 0.013 0.001 TYR A 207 ARG 0.002 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8541 (pttt) cc_final: 0.8334 (pttm) REVERT: A 499 PHE cc_start: 0.7890 (t80) cc_final: 0.7633 (t80) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2278 time to fit residues: 27.0982 Evaluate side-chains 58 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 152 GLN A 275 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.129094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.097814 restraints weight = 4844.898| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.11 r_work: 0.3040 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3777 Z= 0.178 Angle : 0.497 5.600 5103 Z= 0.273 Chirality : 0.040 0.150 573 Planarity : 0.003 0.023 649 Dihedral : 4.325 20.756 502 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.21 % Allowed : 5.41 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.38), residues: 467 helix: 1.81 (0.36), residues: 180 sheet: -0.67 (0.53), residues: 74 loop : 0.42 (0.44), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 432 HIS 0.003 0.001 HIS A 194 PHE 0.011 0.001 PHE A 41 TYR 0.016 0.001 TYR A 207 ARG 0.005 0.001 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.466 Fit side-chains REVERT: A 264 GLU cc_start: 0.8046 (pm20) cc_final: 0.7720 (mp0) REVERT: A 383 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7945 (tt0) REVERT: A 428 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8475 (tt) outliers start: 9 outliers final: 4 residues processed: 61 average time/residue: 0.2200 time to fit residues: 15.9142 Evaluate side-chains 48 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 39 optimal weight: 0.0970 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.128123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.097173 restraints weight = 4812.848| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.07 r_work: 0.3026 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3777 Z= 0.192 Angle : 0.474 5.521 5103 Z= 0.258 Chirality : 0.040 0.180 573 Planarity : 0.003 0.027 649 Dihedral : 4.149 18.856 502 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.21 % Allowed : 6.88 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.38), residues: 467 helix: 1.98 (0.37), residues: 182 sheet: -0.76 (0.53), residues: 74 loop : 0.24 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 432 HIS 0.004 0.001 HIS A 194 PHE 0.013 0.001 PHE A 41 TYR 0.014 0.001 TYR A 207 ARG 0.005 0.001 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.411 Fit side-chains REVERT: A 218 ARG cc_start: 0.6897 (mmm160) cc_final: 0.6487 (mmm160) REVERT: A 383 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: A 428 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8541 (tt) outliers start: 9 outliers final: 6 residues processed: 48 average time/residue: 0.1984 time to fit residues: 11.6490 Evaluate side-chains 48 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 42 optimal weight: 8.9990 chunk 45 optimal weight: 0.0170 chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 26 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.130111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.098739 restraints weight = 4862.851| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.14 r_work: 0.3059 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3777 Z= 0.140 Angle : 0.439 5.445 5103 Z= 0.237 Chirality : 0.039 0.164 573 Planarity : 0.003 0.028 649 Dihedral : 3.913 16.756 502 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.70 % Allowed : 5.41 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.38), residues: 467 helix: 2.06 (0.37), residues: 180 sheet: -0.81 (0.54), residues: 74 loop : 0.20 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 432 HIS 0.002 0.001 HIS A 194 PHE 0.009 0.001 PHE A 41 TYR 0.013 0.001 TYR A 207 ARG 0.004 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.446 Fit side-chains REVERT: A 55 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6327 (pp20) REVERT: A 383 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.8011 (tt0) outliers start: 11 outliers final: 7 residues processed: 54 average time/residue: 0.2038 time to fit residues: 13.3836 Evaluate side-chains 51 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 0.0570 chunk 15 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.128271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.096457 restraints weight = 4949.166| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.17 r_work: 0.3023 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3777 Z= 0.176 Angle : 0.446 6.342 5103 Z= 0.241 Chirality : 0.039 0.161 573 Planarity : 0.003 0.030 649 Dihedral : 3.924 18.379 502 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.70 % Allowed : 7.37 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.38), residues: 467 helix: 2.05 (0.38), residues: 182 sheet: -0.74 (0.54), residues: 74 loop : 0.20 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 432 HIS 0.003 0.001 HIS A 194 PHE 0.008 0.001 PHE A 41 TYR 0.013 0.001 TYR A 207 ARG 0.003 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.443 Fit side-chains REVERT: A 55 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6262 (pp20) outliers start: 11 outliers final: 8 residues processed: 48 average time/residue: 0.2193 time to fit residues: 12.6806 Evaluate side-chains 47 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 495 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 46 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.127562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.096245 restraints weight = 4868.111| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.12 r_work: 0.3015 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3777 Z= 0.181 Angle : 0.446 6.400 5103 Z= 0.241 Chirality : 0.039 0.160 573 Planarity : 0.003 0.030 649 Dihedral : 3.928 18.165 502 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.70 % Allowed : 7.37 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.38), residues: 467 helix: 1.90 (0.37), residues: 186 sheet: -0.68 (0.55), residues: 74 loop : 0.20 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 432 HIS 0.002 0.001 HIS A 194 PHE 0.018 0.001 PHE A 41 TYR 0.013 0.001 TYR A 207 ARG 0.004 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.419 Fit side-chains REVERT: A 55 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6193 (pp20) outliers start: 11 outliers final: 8 residues processed: 45 average time/residue: 0.2260 time to fit residues: 12.2152 Evaluate side-chains 48 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 495 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.127632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.096221 restraints weight = 4876.283| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.13 r_work: 0.3012 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3777 Z= 0.184 Angle : 0.451 6.957 5103 Z= 0.242 Chirality : 0.039 0.160 573 Planarity : 0.003 0.030 649 Dihedral : 3.943 18.564 502 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.21 % Allowed : 8.11 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.38), residues: 467 helix: 1.90 (0.37), residues: 186 sheet: -0.75 (0.56), residues: 74 loop : 0.16 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 432 HIS 0.002 0.001 HIS A 194 PHE 0.016 0.001 PHE A 41 TYR 0.012 0.001 TYR A 207 ARG 0.005 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.406 Fit side-chains REVERT: A 23 ASP cc_start: 0.8240 (t70) cc_final: 0.7914 (t0) REVERT: A 27 ARG cc_start: 0.8494 (mtt90) cc_final: 0.8225 (mtt90) REVERT: A 55 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6181 (pp20) outliers start: 9 outliers final: 7 residues processed: 49 average time/residue: 0.1997 time to fit residues: 12.1127 Evaluate side-chains 49 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 495 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.0370 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.128181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.097992 restraints weight = 4900.628| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.04 r_work: 0.3033 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3777 Z= 0.172 Angle : 0.459 8.575 5103 Z= 0.245 Chirality : 0.039 0.157 573 Planarity : 0.003 0.031 649 Dihedral : 3.873 17.782 502 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.70 % Allowed : 8.85 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.38), residues: 467 helix: 2.08 (0.38), residues: 180 sheet: -0.76 (0.56), residues: 74 loop : 0.09 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 432 HIS 0.002 0.001 HIS A 194 PHE 0.007 0.001 PHE A 41 TYR 0.012 0.001 TYR A 207 ARG 0.004 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.441 Fit side-chains REVERT: A 55 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6182 (pp20) outliers start: 11 outliers final: 9 residues processed: 47 average time/residue: 0.1907 time to fit residues: 11.1041 Evaluate side-chains 50 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 495 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 8 optimal weight: 0.0470 chunk 5 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.128734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.097274 restraints weight = 4809.773| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.10 r_work: 0.3037 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3777 Z= 0.170 Angle : 0.465 9.224 5103 Z= 0.246 Chirality : 0.039 0.156 573 Planarity : 0.003 0.031 649 Dihedral : 3.869 17.730 502 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.46 % Allowed : 9.58 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.38), residues: 467 helix: 1.79 (0.38), residues: 188 sheet: -0.79 (0.57), residues: 74 loop : 0.23 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 432 HIS 0.002 0.001 HIS A 194 PHE 0.014 0.001 PHE A 455 TYR 0.012 0.001 TYR A 207 ARG 0.004 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.402 Fit side-chains REVERT: A 55 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6172 (pp20) outliers start: 10 outliers final: 8 residues processed: 46 average time/residue: 0.1981 time to fit residues: 11.1733 Evaluate side-chains 48 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 495 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 0.0470 chunk 15 optimal weight: 0.6980 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.128582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.097116 restraints weight = 4845.224| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.12 r_work: 0.3031 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3777 Z= 0.176 Angle : 0.486 9.838 5103 Z= 0.256 Chirality : 0.039 0.156 573 Planarity : 0.003 0.032 649 Dihedral : 3.846 17.753 502 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.21 % Allowed : 10.32 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.38), residues: 467 helix: 1.96 (0.38), residues: 182 sheet: -0.84 (0.57), residues: 74 loop : 0.17 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 432 HIS 0.002 0.001 HIS A 194 PHE 0.014 0.001 PHE A 287 TYR 0.012 0.001 TYR A 207 ARG 0.004 0.001 ARG A 222 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.413 Fit side-chains REVERT: A 55 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6178 (pp20) outliers start: 9 outliers final: 8 residues processed: 43 average time/residue: 0.1958 time to fit residues: 10.3746 Evaluate side-chains 49 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 495 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.127574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.096025 restraints weight = 4881.620| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.11 r_work: 0.3017 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3777 Z= 0.206 Angle : 0.501 9.968 5103 Z= 0.264 Chirality : 0.040 0.158 573 Planarity : 0.004 0.032 649 Dihedral : 3.943 18.852 502 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.97 % Allowed : 10.32 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.38), residues: 467 helix: 1.97 (0.38), residues: 182 sheet: -0.75 (0.58), residues: 72 loop : 0.13 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 432 HIS 0.002 0.001 HIS A 194 PHE 0.018 0.001 PHE A 455 TYR 0.012 0.001 TYR A 207 ARG 0.005 0.001 ARG A 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2416.40 seconds wall clock time: 43 minutes 45.23 seconds (2625.23 seconds total)